


Through the Stargate

by Fnuggi



Category: Mass Effect, Stargate Atlantis
Genre: M/M, unbetaed
Language: English
Status: In-Progress
Published: 2016-08-21
Updated: 2017-06-19
Packaged: 2018-08-10 05:38:25
Rating: Teen And Up Audiences
Warnings: No Archive Warnings Apply
Chapters: 3
Words: 3,371
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/7832452
Author URL: https://archiveofourown.org/users/Fnuggi/pseuds/Fnuggi
Summary: <blockquote class="userstuff">
              <p>After the destruction of the Alpha relay, the Alliance decides to send John away to their new outpost: Atlantis.</p>
            </blockquote>





	1. Chapter 1

**Author's Note:**

> This has been sitting in my drafts for SO long, and I finally worked up the courage to actually post it here.
> 
> I'm not entirely happy with the final scene, but I've left this unfinished for so long now, I really just wanted to get it done.
> 
> I also want to give a big shout-out to my friend, Vic, who has been an absolutely invaluable help in coming up with this story.
> 
> As always, comments and feedback are greatly appreciated.
> 
> You can also find me over on tumblr @ jaylahz.

_ “Oh my god, is that commander Shepard?” _

_ “What’s he doing here? Shouldn’t he be out fighting the reapers?” _

The whispers were not lost on John as he moved through the hallways of the Antarctic outpost, but he choose to ignore them. It wasn’t easy. Most people had heard some version of what had happened in the Bahak system and they probably had opinions on it too.

He didn’t care.

John wasn’t even supposed to be here in the first place. The only reason he was, was because the Alliance had decided to let him take the fall for the destruction of the Alpha relay.

While he did regret the massive loss of life his actions had caused, he could not bring himself to feel sorry for destroying the relay. It had bought them more time to prepare for the reapers.

And then the Alliance had sent him away.

Just thinking about it made John’s blood boil.

It must have been showing on his face, because people were quick to move out of his way as he walked towards the sickbay. The medical exam was standard procedure for all Alliance personnel when they were assigned to a new post, so John expected it to be over quickly.

Sickbay was just as busy as the rest of the base when John arrived. He was directed to one of the beds by a nurse and instructed to sit down. As she worked, John looked around, taking in the room.

The sickbay was a rectangular room with beds along both sides. The room was filled with people, most of whom were medical personnel. A few other people seemed to be getting their physicals too.

Suddenly, John froze. A familiar Scottish accent could be heard over the murmur of conversation and John was sure he knew who it belonged to.  


 

* * *

 

_ Pain. That was the first thing he registered. There wasn't a part of his body that didn’t feel like it was on fire and John could feel his heart beating rapidly. _

_ “He’s reacting to outside stimuli” John had no idea who the person speaking was, but the note of alarm in their voice did not go unnoticed. He didn't know why, but the man’s Scottish accent was one of the only other things that his mind seemed to register. _

_ “Damn it, he’s not ready yet. give him the sedative” Before John could even think to ask what was going on, he felt a prick in his arm and then nothing. _

 

* * *

 

 

_ John was moving through the base, taking down any security mechs he encountered. Beside him, Jacob Taylor was using his biotics to do the same. _

_ They had found Wilson on their way through the base and John had decided to help him. However, John’s gut told him that something was off, but he couldn’t put his finger on what it was. _

_ “We’re almost there” Wilson said, stopping in front of the door that lead to the shuttle bay. Just then, the door slid open to reveal two people. _

_ Although he didn’t know their names, John recognized the couple as the two people he had seen the first time he’d woken up. The man seemed to be very distressed by the whole situation, but the woman had a fierce scowl on her face. _

_ “Miranda, you-” Before any of them could do anything, Miranda had pulled her gun and shot Wilson in the head. _

_ “What the hell are you doing Miranda?!” Jacob exclaimed. _

_ “My job. Wilson betrayed us” She replied, holstering her gun. _

_ “Even if you’re sure, did he really deserve that?” John asked. _

_ “He sabotaged the security system, killed my staff and he would have killed us. So yes, I think he deserved it” Miranda said. _

_ “I knew something was off about him” John said, lowering his gun slightly. “So, what’s our next step?” _

_ “We get on that shuttle and get the hell out of here” Miranda responded. _

 

* * *

 

_ John closed his eyes and leaned back against the wall of the shuttle. Miranda and Jacob were sitting across from him and next to him was the doctor whose name he still didn’t know. _

_ Maybe it was wrong of him, but John felt a small measure of relief at the fact that doctor Beckett looked as terrible as he was feeling. _

_ John was still trying to wrap his mind around the fact that he had lost two years of his life. He supposed that the fact that both the Alliance and the council had given up on him shouldn’t come as a surprise. _

_ And yet, it did. _

_ It seemed that all the work he had put into stopping Saren had been for nothing. Apparently, the council had brushed everything under the carpet after he had been declared dead. That didn’t surprise him. _

_ It would seem that he was back to square one. _

_ Miranda had questioned him about his old life and John was glad to find that all his memories were still there. But now that they were done, a quiet had settled over the shuttle. _

_ John didn’t like the fact that it was Cerberus who had brought him back. He had had several run-ins with them in the past, which had more often than not ended with a high body count. Most times, it had been Cerberus’ people. _

_ Miranda had said that The Illusive Man wanted to talk to him and it seemed that he had no other choice than to go along with it. John didn’ like it, but he needed answers. Answers that he hoped The Illusive Man could give him. _

 

* * *

 

Although he had travelled all over the galaxy while working for the Alliance, John was still unsure of what he should be feeling as he stood in front of the gate. Despite the limited space in the gateroom, people seemed to be giving him a wide berth.

John shifted uncomfortably. He missed the crew of the Normandy. Here, everyone knew of him and what he’d done and they all expected something of him.

There had been expectations back on the Normandy too, but it had been different. Every single member of the Normandy’s crew had become family to him in some way and it made dealing with the crew’s expectations easier.

John blinked when the wormhole materialized in the stargate. He had seen a lot in his time, but never anything like this.

As the probe was sent through the gate, John raised his rifle. For several long moments, the only sounds that could be heard in the gateroom, were those of the technicians calling out various instructions.

Finally, the signal for them to start going through the gate was given and as John moved towards the event horizon, he wondered what exactly they would find on the other side.


	2. Chapter 2

**Notes for the Chapter:**

> Oh my god, this chapter just would NOT co-operate with me x_x
> 
> I know these first few chapters are sticking very closely to the events of the show, but I will try to write in mor original content as I go along.
> 
> as always, kudos and reviews are greatly appreciated :D I love hearing what you guys think.

Of course, things couldn’t just be easy.

The passage through the gate had been easy, but once they had emerged on the other side, they had realized that Atlantis was under several hundred feet of water.

John watched helplessly as another part of the shield protecting the city failed. If this kept happening, they would all soon drown.

“We need to evacuate as soon as possible” Rodney said. Even though all the teams that had been exploring the city had been recalled to the gateroom, the damage had been done.

“No!” Elizabeth, the leader of the expedition was speaking. “We only just found this place. We can’t abandon it”

“It’s only a matter of time before the shield collapses entirely and the ocean comes crashing in on us. It’s not like we have much of a choice” John retorted. Every minute they spend arguing was a minute less to evacuate.

For a long moment, Elizabeth was silent. Then she spoke.

“All right. Where do you suggest we go?” She asked, turning to Rodney.

“Anywhere but here. We just need a gate address and we could go right now” He replied.

“Commander Sumner, I want you to take a team through the gate, Once you’ve secured the area, you’ll send a message back through the gate so we’ll know it’s safe to come through” The man in question nodded and motioned for John to follow him.

 

* * *

 

“You truly can not return to your own world?” John looked up and saw Teyla approaching. The Athosians had been welcoming, if a bit cautious of them at first and John didn’t blame them.

He had been standing near the edge of the lake that the Athosians had camped near and when Teyla came over, the other two men gave John an odd look and walked away.

“No” John replied.

“Then there’s something you need to see” Teyla said and motioned for John to follow her.

 

* * *

 

“Where are we going?” They had been walking through the woods for some time now. Teyla was moving with a grace that John found hard to match.

“It is not far” Teyla said as she kept walking. She seemed to know exactly where she was going, so John just followed her.

Finally, he spotted a cave up ahead. It seemed to be where Teyla was leading him and it made John wonder exactly what was inside.

Inside the cave were a series of crude drawings depicting groups of people being taken by strange, alien looking ships.

“This is where the survivors hid from the wraith” Teyla said, looking at the drawings. “These drawings date back thousands of years, to a time before our great city was destroyed”

Looking around, John saw that there were a drawing of a city on one of the walls. It must have been beautiful in its time, he thought. “So, this represents the destruction of your city, right?” John asked, his attention drawn to another drawing.

“Yes” Teyla answered.

“So… You’re telling me that this has happened before?” John inquired. This was starting to sound a little too familiar.

“I believe that it has happened many times before. The last great holocaust was five generation ago, but still they come in smaller numbers to remind us of their presence” The sadness in Teyla’s voice was not lost on John.

“How do you live like that?”

“We move our hunting camps around and try to teach our children not to live in fear. But… It is hard” Teyla replied.

“That’s a hell of a way to live” John commented.

"It is hard, but we manage" Teyla said. “I heard some of your people talk about something called reapers” 

“Yeah” John replied and then added: “They’re kind of like the wraith, except they only come once every fifty thousand years to wipe out all organic life in our galaxy”

“And you believe they will return?”

“Yeah. The worst part about it all is, that I’m one of the few people who do” John sighed. It had been an uphill battle from day one, but after the defeat of Sovereign, the council had started listening to him.

But that had changed when he had died.

Both the Alliance and the Council had spent the two years he’d been dead sweeping everything under the rug, and the fact that John had been brought back to life by Cerberus had only made them all the more eager to forget everything.

Learning that his friends had moved on with their lives had been hard for John to take.

Meeting Kaidan again on Horizon had been even harder.John had tried to explain the situation to him, but Kaidan hadn’t been willing to listen. So they had parted ways on bad terms.

Everything after John had defeated the collectors and handed himself over to the Alliance had happened so fast, there’d been no time for the two of them to talk.

“Everyone’s expecting me to save them but I’m… I’m not sure I can” John admitted softly. It felt good to be able to talk about it with someone who had no expectations of him. Someone who knew nothing of the war and the reapers.

Teyla regarded him for a moment before speaking. “You should look to the people around you. They will help you the most”

John felt a small smile forming on his face. Teyla may not know anything about the war, but the words were still comforting.

Most people seemed to be unaware that the victory against the collectors hadn’t been his alone. It had been a team effort.

John’s relationship with some of the crewmembers of the SR2 had been rocky, to put it mildly, at first. It was especially true for his relationship with his second-in-command, Miranda and, to a lesser extend, Jacob Taylor.

At the time, they had both been loyal Cerberus operatives and because of this, John had been unsure whether or not he could trust them. But they had ultimately turned out to be great crewmembers and even greater friends.

Luckily, Tali, Garrus, Joker and doctor Chakwas had all been around as well, so it hadn’t been all bad.

“Right” John was unsure how he’d do it. All the people in Atlantis knew of him, and they all expected so much of him. There were days where John wished he’d never come into contact with the beacon, that saving the galaxy was someone else’s job. But even if that had been the case, John knew he wouldn’t have been able to sit idly by.

“We should head back” Teyla said and started to leave. John, throwing one last glance at the drawings, followed her.

 

* * *

 

They were about half way back to the village when they heard it. Moments before, Teyla had stopped moving, and then, a high pitched whine could be heard overhead.

“The wraith!” With that, Teyla started running.


	3. Chapter 3

The sight of innocent people caught in the crossfire was something John would never get used to. As he was moving through the camp, he noticed that there was a surprisingly low number of bodies on the ground. It seemed that the wraith wanted to take people alive so that they could feed on them.

The thought made John feel sick.

Add to that the fact that Teyla had been taken by the wraith, and, well… John’s day just kept getting better and better.

“Someone help me!” John heard the young boy’s voice over the high-pitched whine of the wraith darts. He recognized the boy from earlier that day. It was Halling’s son, Jinto and behind him was a wraith.

“Head to the gate!” John shouted as his biotics flared. With as much power as he could muster, John used his biotics to tear into the wraith. Then, with one last look at the burning village, John started towards the gate himself.

 

* * *

 

Flying the jumper was unlike anything John had ever done. It was as if the ship was reading his mind.

Convincing Elizabeth to let him and a few others go on this rescue mission hadn’t been easy. It wasn’t until John and one of the scientists named Rodney had found the jumper bay that she had agreed to it, and even then, she still wasn't happy about it.

Being able to actually do something had been a relief for John. The idea of leaving someone behind didn’t seem right to him, even if it was someone he had known for less than a day. The fact that they were going in almost completely blind felt wrong, but they had to get their people back.

The bump of the jumper hitting the ground brought him back to the present.

“All right, listen up” John had turned to the other people in the jumper as he spoke. “It’ll be me and Lieutenant Ford going in to get the prisoners. The rest of you will be staying out here to keep an eye out for incoming enemies”

A chorus of ‘yes sir’s sound from the other people.

As John exits the jumper, Lieutenant Ford follows him.

They’re lucky that the jumpers seem to be equipped with the Atlantis equivalent of a lifesign detector. If John was reading it correctly, there was very little activity aboard the ship.

That in itself was enough to make John’s skin crawl. But luckily, there was also a group of five life signs close together and if John had to guess, that was their people.

Getting into the ship was easy enough, and that was another thing that set John on edge. It was too easy.

John kept checking the life signs detector as they moved through the dark corridors of the ship towards the prison cells. But of course, things could not just go according to plan.

“Commander!” It was Teyla. Her voice was an urgent whisper, as if she was afraid that the wraith would come if she raised her voice. “The wraith took colonel Sumner”

“What? when?” John asked.

“Not long ago” john swore under his breath. They needed a change of plans, fast.111 

“Alright, here’s the plan” John said as he began to place explosives around the cell door. “I’m gonna go look for colonel Sumner and if I’m not back in an hour, you blow this place and get out of here”

 

* * *

He hadn’t been able to save colonel Sumner.

The thought kept repeating itself in John’s mind, even as people around him celebrated the successful rescue of the people whom had been taken by the wraith.

John was leaning on the railing of the balcony, watching the dark ocean. Even through the noise of people talking, the sound of the ocean lapping against the city could be heard. Having grown up in one of Earth’s major cities, it was a sound that John had never heard growing up, but it was one he thought he could get used to.

“The view really is something, isn’t it?” John startled as Elizabeth came up to him, two cups in her hands.

“Yeah” John replied, taking the cup Elizabeth offered him. Even at night, the reflected light of the stars in the sea was a beautiful sight and for a while, they just stood there, taking it in.

“You did good today, John” Elizabeth said.

“I wasn’t able to save Colonel Sumner” John sighed.

“Maybe not, but look around. All these people are safe because of what you did today”

John turned to look at the crowd. A table had been set out with food, some of it Athosian and some of it human. Around them, people were talking quietly and the general mood was happy and relaxed. Before John could say anything, Teyla had walked over to them.

“Doctor Weir is right” She said. “You’ve saved a great number of people today, even if colonel Sumner was not one of them” Teyla placed both her hands on John’s shoulders and bowed her head. After a moment of uncertainty, John bowed his head, touching his forehead to hers.

“You have earned both my friendship and that of my people. And with our help, you will make many more friends” Teyla raised her head again as she spoke.

John hoped so. It was bad enough that there were several alien races back in the milky way hellbent on destroying humanity. It was nice to know, that at least one of the new people they had met out here was friendly.

He and Elizabeth both watched Teyla as she walked away from them to talk to some of her own people.

John’s eyes briefly landed on doctor Beckett who was with doctor McKay and a few others, but he quickly looked away again. The memories associated with the doctor wasn’t something he wished to dwell on.

At least not tonight.

“To colonel Sumner” Elizabeth had raised her cup in a toast.

“To colonel Sumner” John repeated, raising his own cup. He wasn’t sure what exactly it was he was drinking, but it had a pleasant burn to it.

After he had finished his drink, he turned his attention back to the ocean. The chatter of the people around him faded into the background as John let his mind wander.

No, he may not have been able to save colonel Sumner and he wasn’t happy about that, but Elizabeth had been right. A lot of people were alive because of what he had done and for now, that would have to be enough. 

**Notes for the Chapter:**

> This chapter has been sitting unfinished in my drafts for a really long time, and I only just managed to finish it.
> 
> rest assured, though, that this story hasn't been abandoned - it's just taking me a long time to write it.


End file.
